Overview

This report summarizes the results of the Association module for phosphoproteome at FDR < 0.01. The association module runs several marker selection algorithms on each comparison pair to assign a combined score identifying the best markers. ssGSEA is then run on these marker results to identify significantly enriched pathways. Detailed documentation for the association analysis module can be found here and for the ssGSEA module here.

ssGSEA Association Results

Please note that all volcano plots are interactive; hover mouse over a given point to see which pathway it corresponds to.

ER Status

Figure: Interactive volcano plot summarizing ssGSEA pathway results for ER Status, contrast Positive over Negative. X axis represents the Normalized Enrichment Score (NES) for Positive over Negative; positive NES values indicate enrichment in Positive and negative NES values indicate enrichment in Negative. Y axis represents the -log10 of the FDR value. Results above the dashed line are significant at FDR cutoff = 0.01.

Table: 14 significantly enriched pathways for Positive over Negative with FDR < 0.01.

GATA3 mutation

Figure: Interactive volcano plot summarizing ssGSEA pathway results for GATA3 mutation, contrast X1 over X0. X axis represents the Normalized Enrichment Score (NES) for X1 over X0; positive NES values indicate enrichment in X1 and negative NES values indicate enrichment in X0. Y axis represents the -log10 of the FDR value. Results above the dashed line are significant at FDR cutoff = 0.01.

No significantly enriched pathways for X1 over X0 with FDR < 0.01.

PAM50

Contrast: Basal vs rest

Figure: Interactive volcano plot summarizing ssGSEA pathway results for PAM50, contrast Basal vs rest. X axis represents the Normalized Enrichment Score (NES) for Basal vs rest; positive NES values indicate enrichment in Basal and negative NES values indicate enrichment in rest. Y axis represents the -log10 of the FDR value. Results above the dashed line are significant at FDR cutoff = 0.01.

Table: 11 significantly enriched pathways for Basal vs rest with FDR < 0.01.

Contrast: Her2 vs rest

Figure: Interactive volcano plot summarizing ssGSEA pathway results for PAM50, contrast Her2 vs rest. X axis represents the Normalized Enrichment Score (NES) for Her2 vs rest; positive NES values indicate enrichment in Her2 and negative NES values indicate enrichment in rest. Y axis represents the -log10 of the FDR value. Results above the dashed line are significant at FDR cutoff = 0.01.

No significantly enriched pathways for Her2 vs rest with FDR < 0.01.

Contrast: LumA vs rest

Figure: Interactive volcano plot summarizing ssGSEA pathway results for PAM50, contrast LumA vs rest. X axis represents the Normalized Enrichment Score (NES) for LumA vs rest; positive NES values indicate enrichment in LumA and negative NES values indicate enrichment in rest. Y axis represents the -log10 of the FDR value. Results above the dashed line are significant at FDR cutoff = 0.01.

Table: 12 significantly enriched pathways for LumA vs rest with FDR < 0.01.

Contrast: LumB vs rest

Figure: Interactive volcano plot summarizing ssGSEA pathway results for PAM50, contrast LumB vs rest. X axis represents the Normalized Enrichment Score (NES) for LumB vs rest; positive NES values indicate enrichment in LumB and negative NES values indicate enrichment in rest. Y axis represents the -log10 of the FDR value. Results above the dashed line are significant at FDR cutoff = 0.01.

Table: 16 significantly enriched pathways for LumB vs rest with FDR < 0.01.

Overview of all contrasts

Figure: Heatmap summarizing significant ssGSEA pathway results for PAM50, all contrasts, clustered by Hallmark process category. Asterisk denotes a significant result at FDR cutoff = 0.01.

PIK3CA mutation

Figure: Interactive volcano plot summarizing ssGSEA pathway results for PIK3CA mutation, contrast X1 over X0. X axis represents the Normalized Enrichment Score (NES) for X1 over X0; positive NES values indicate enrichment in X1 and negative NES values indicate enrichment in X0. Y axis represents the -log10 of the FDR value. Results above the dashed line are significant at FDR cutoff = 0.01.

Table: 14 significantly enriched pathways for X1 over X0 with FDR < 0.01.

PR Status

Figure: Interactive volcano plot summarizing ssGSEA pathway results for PR Status, contrast Positive over Negative. X axis represents the Normalized Enrichment Score (NES) for Positive over Negative; positive NES values indicate enrichment in Positive and negative NES values indicate enrichment in Negative. Y axis represents the -log10 of the FDR value. Results above the dashed line are significant at FDR cutoff = 0.01.

Table: 10 significantly enriched pathways for Positive over Negative with FDR < 0.01.

TP53 mutation

Figure: Interactive volcano plot summarizing ssGSEA pathway results for TP53 mutation, contrast X1 over X0. X axis represents the Normalized Enrichment Score (NES) for X1 over X0; positive NES values indicate enrichment in X1 and negative NES values indicate enrichment in X0. Y axis represents the -log10 of the FDR value. Results above the dashed line are significant at FDR cutoff = 0.01.

Table: 11 significantly enriched pathways for X1 over X0 with FDR < 0.01.